TSD composition, length distribution, and inverted/truncated elements. (A) A sequence logo representation of the 5′ flank junction for TSDs ≥10 bp (n = 37) without ambiguities. The cartoon underneath represents the junction position relative to the RPC. (B) TSD length distribution of RPCs (n = 116). (C) An HMGN1 RPC 5′-truncated at bp 152 and inverted at bp 299–316 (gi 16160227, bp 1,018,816–1,019,883). (D) An HMGN2 PS 5′-truncated at bp 788 and inverted at bp 938–959 (gi 16157330, bp 297,023–297,461). This sequence has a TSD and a poly(A) tract, most likely an RPC; see text. Numbers correspond to position in the HMG mRNA; (triangles) TSDs; (thin arrows) direction of corresponding HMG transcript.